9R0Q | pdb_00009r0q

Paraoxonase-1 in complex with terbium(III) and 2-hydroxyquinoline

• PDB DOI: https://doi.org/10.2210/pdb9R0Q/pdb

• Classification: HYDROLASE
• Organism(s): Oryctolagus cuniculus
• Expression System: Escherichia coli B
• Mutation(s): Yes 


• Deposited: 2025-04-24 Released: 2025-08-06 
• Deposition Author(s): Smerkolj, J., Pavsic, M., Golicnik, M.
• Funding Organization(s): Slovenian Research Agency

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 
  0.229 (Depositor), 0.229 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Starting Model: experimental

Literature

Intramolecular sensitization and structure of a Tb 3+ /2-hydroxyquinoline conjugate in the paraoxonase 1 active site.

Smerkolj, J., Bahun, M., Poklar Ulrih, N., Bavec, A., Pavsic, M., Golicnik, M.

(2025) Dalton Trans 54: 12471-12481

• PubMed: 40735812 
• DOI: https://doi.org/10.1039/d5dt01484k
• Primary Citation of Related Structures:  
  9R0Q


• PubMed Abstract: 
  

  Paraoxonase 1 (PON1) is a Ca ²⁺ -dependent enzyme involved in oxidative stress processes and is widely studied for its protective roles in various diseases. Intermolecular sensitization of lanthanide ions was implemented by replacing Ca ²⁺ ions from the recombinant PON1 (rePON1) catalytic site in the presence of 2-hydroxyquinoline (2HQ) as an external antenna. Although the replacement of Ca ²⁺ ions with lanthanide ions indicates weaker binding affinity for the coordination of 2HQ in the protein milieu of the rePON1 active site, it results in the formation of a highly emissive supramolecular complex in the case of Tb ³⁺ ions. The architecture of the ternary rePON1 : Tb ³⁺  : 2HQ conjugate, which allows efficient terbium sensitization and its specific long-wavelength metal phosphorescence emission, was resolved by X-ray crystallography. These findings could establish a non-catalytic quantification strategy for PON1 and provide additional structural insights into lanthanide substitution in this Ca ²⁺ -dependent enzyme.

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Organizational Affiliation: 
• University of Ljubljana, Faculty of Medicine, Institute of Biochemistry and Molecular Genetics, Vrazov trg 2, 1000 Ljubljana, Slovenia. [e-mail].
University of Ljubljana, Biotechnical Faculty, Department of Food Science and Technology, Jamnikarjeva 101, 1000 Ljubljana, Slovenia.
University of Ljubljana, Faculty of Chemistry and Chemical Technology, Department of Chemistry and Biochemistry, Večna pot 113, 1000 Ljubljana, Slovenia.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 41 kDa 
• Atom Count: 2,765 
• Modeled Residue Count: 338 
• Deposited Residue Count: 360 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serum paraoxonase/arylesterase 1	A	360	Oryctolagus cuniculus	Mutation(s): 1  Gene Names: PON1, PON EC: 3.1.1.2 (PDB Primary Data), 3.1.1.81 (PDB Primary Data), 3.1.8.1 (PDB Primary Data)
UniProt
Find proteins for P27170 (Oryctolagus cuniculus) Explore P27170  Go to UniProtKB:  P27170

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TB (Subject of Investigation/LOI)	B [auth A], C [auth A]	TERBIUM(III) ION Tb HKCRVXUAKWXBLE-UHFFFAOYSA-N
OCH	F [auth A], G [auth A]	QUINOLIN-2(1H)-ONE C9 H7 N O LISFMEBWQUVKPJ-UHFFFAOYSA-N
BR	H [auth A], I [auth A]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M
CA	D [auth A], E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free:  0.229 (Depositor), 0.229 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Diffraction Data: https://doi.org/10.34965/i32532

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.064	α = 90
b = 98.064	β = 90
c = 138.877	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-08-06 
Deposition Author(s): Smerkolj, J., Pavsic, M., Golicnik, M.

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Funding Organization	Location	Grant Number
Slovenian Research Agency	Slovenia	P1-0170
Slovenian Research Agency	Slovenia	55728
Slovenian Research Agency	Slovenia	P1-0140

Revision History  

• Version 1.0: 2025-08-06
  Type: Initial release
  
• Version 1.1: 2025-08-13
  Changes: Database references
• Version 1.2: 2025-08-27
  Changes: Database references